Publications

Take a look at the most recent publications by our team members.

2025

Heuristic energy-based cyclic peptide design

PLoS Computational Biology, 30 Apr 2025, 21(4):e1012290
Zhu Q, Mulligan VK, Shasha D

CyclicCAE: A Conformational Autoencoder for Efficient Heterochiral Macrocyclic Backbone Sampling

bioRxiv, 2025, pp. 2025.02. 21.639569
Powers AC, P Renfrew PD, Hosseinzadeh P,  Mulligan VK

2024

High-resolution epitope mapping of commercial antibodies to ANCA antigens by yeast surface display

Journal of Immunological Methods, 2024, pp. 113654
Poulton JS, Lamba S, Free M, Xi G,  McInnis E, Williams G, Kudlacek ST, Thieker D, Kuhlman B, Falk R

Ultra-confined controllable cyclic peptides as supramolecular biomaterials

Nano Today, 2024, pp. 102247
Chorsi M, Linthicum W, Pozhidaeva A, Mundrane C, Mulligan VK, Chen Y, Tavousi P, Gorbatyuk V, Vinogradova O, Hoch JC, Huey BD, Nguyen TD, Soh HT, Kazerounian K, Ilies H

Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins

PLOS Computational Biology, 2024, pp. e1011939
Ertelt M, Mulligan VK, Maguire JB, Lyskov S, Moretti R, Schiffner T, Meiler J, Schoeder CT

Heteropolymer modelling and design incorporating quantum chemistry with RosettaQM

APS March Meeting Abstracts, 2024, pp. W55. 008
Mulligan VK, Turzo B, P, Renfrew D, Jurich C, Brown B

2023

Macrocyclic polypeptides

Patent Pub. No. : US2023/0303626 A1
Hosseinzadeh P, Baker D, Bhardwaj G, Mulligan VK

De novo designed mixed chirality peptide macrocycles with internal symmetry

Patent Pub. No. : US2023/0279054 A1
Mulligan VK, Kang C, Craven T, Baker D

Macromolecular modelling algorithms harnessing quantum computation

APS March Meeting Abstracts, pp. Y72. 014
Mulligan VK, Pandey M, Zaborniak T, Galda A, Melo H

Population dynamics of immunological synapse formation induced by bispecific T cell engagers predict clinical pharmacodynamics and treatment resistance

eLife, 2023
Liu, Zhou, Kudlacek, Qi, Dunlap, Cao

2022

Macrocyclic polypeptides

Patent No.: US 11,524,979 B2
Hosseinzadeh P, Baker D, Bhardwaj G, Mulligan VK

Accurate de novo design of membrane-traversing macrocycles

Cell, 2022, pp. 3520-3532. e26
Bhardwaj G, O’Connor J, Rettie S, Hua Huang Y, Ramelot TA, Mulligan VK, Alpkilic GC, Palmer J, Bera AK, Bick MJ, Di Piazza M, Li X, Hosseinzadeh P, Craven TW, Tejero R, Lauko A, Choi R, Glynn C, Dong L, Griffin R, van Voorhis WC, Rodriguez J, Stewart L, Montelione GT, Craik D, Baker D

Rational design of rigidly-folded peptide macrocycle therapeutics using classical and quantum computers

Journal of peptide science, 2022, v. 28
Mulligan VK

Correction to “the rosetta all-atom energy function for macromolecular modeling and design”

Journal of chemical theory and computation, 2022, pp. 4594-4594
Alford RF, Leaver-Fay A, Jeliazkov JR, O’Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack Jr RL, Das R, Baker D, Kuhlman B, Kortemme T, Gray JT

Designing new peptide and protein therapeutics using adiabatic quantum annealers

APS March Meeting Abstracts, 2022, B01. 005
Mulligan VK, Melo H, Merritt H, Sawaya M, Slocum S, Weitzner B, Watkins A, Renfrew PD, Pelissier C, Yeates T, Arora P, Bonneau R, Pandey M, Galda A

Peptide design with quantum approximate optimization algorithm

APS March Meeting Abstracts, 2022, B01. 004
Galda A, Mulligan VK,  MacCormack I, Crooks G, Melo H

"Computational Design of Peptide-Based Binders to Therapeutic Targets", Approaching the Next Inflection in Peptide Therapeutics: Attaining Cell Permeability and Oral Bioavailability

American Chemical Society, 2022, pp. 55-102
Mulligan VK, Hosseinzadeh P

"How to Design Peptides", Chemokine-Glycosaminoglycan Interactions: Methods and Protocols

Springer US, 15 Nov 2022
Dodd-o J, Acevedo-Jake AM, Azizogli A, Mulligan VK, Kumar VA

Multibody molecular docking on a quantum annealer

arXiv:2210.11401., 20 Oct 2022
Mohit Pandey, Tristan Zaborniak, Hans Melo, Alexey Galda, Vikram K. Mulligan

"Computational methods for peptide macrocycle drug design", Peptide therapeutics: fundamentals of design, development, and delivery

Springer International Publishing, 27 Sept 2022
Mulligan VK

Stabilizing proteins, simplified: A Rosetta‐based webtool for predicting favorable mutations

Protein Science, 21 Sept 2022
Thieker DF, Maguire JB, Kudlacek ST, Leaver-Fay A, Lyskov S, Kuhlman B

Accurate de novo design of membrane-traversing macrocycles

Cell, 15 Sept 2022
Bhardwaj G, O’Connor J, Rettie S, Huang Y,  Ramelot TA, Mulligan VK, Alpkilic GC, Palmer J, Bera AK, Bick MJ, Di Piazza M, Li X, Hosseinzadeh P, Craven TW, Tejero R, Lauko A, Choi R, Glynn C, Dong L, Griffin R, van Voorhis WC, Rodriguez J, Stewart L, Montelione GT, Craik D, Baker D

Ancestral Sequence Reconstruction and Alternate Amino Acid States Guide Protein Library Design for Directed Evolution

Methods in Molecular Biology, 29 Apr 2022
VanAntwerp J, Finneran P, Dolgikh B, Woldring D

2021

Designed, highly expressing, thermostable dengue virus 2 envelope protein dimers elicit quaternary epitope antibodies

Science Advances, 15 Oct 2021
Stephan Kudlacek, Stefan Metz, Devina Thiono, Alexander M Payne, et al.

XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers

PLOS Comp Bio, 27 Sep 2021
Maguire JB, Grattarola D, Mulligan VK, Klyshko E, Melo H

Perturbing the energy landscape for improved packing during computational protein design

Proteins: Structure, Function, and Bioinformatics, May 2021
Jack B. Maguire,Hugh K. Haddox,Devin Strickland,Samer F. Halabiya, et al.

Augmenting QAOA Ansatz with Multiparameter Problem-Independent Layer.

arXiv preprint arXiv:2205.01192
Chalupnik, M., Melo, H., Alexeev, Y., & Galda, A

Structure-Guided Stabilized DENV2 Envelope Subunit Vaccine Elicits DENV2 Neutralizing Antibody In Vivo

American Journal of Tropical Medicine and Hygiene, 01 Nov 2021
Thiono DJ, Kudlacek ST, Samaras DL, Tian S, McCracken MK, Soman SA, Gromowski GD, Jarman RG, Forsberg J, Phan TT, Kuhlman B, de Silva AM

Multibody molecular docking on a quantum annealer

arXiv:2210.11401., 20 Oct 2022
Mohit Pandey, Tristan Zaborniak, Hans Melo, Alexey Galda, Vikram K. Mulligan

Current directions in combining simulation-based macromolecular modeling approaches with deep learning

Expert Opin Drug Discov., Sep 2021
Vikram Khipple Mulligan

The Emerging Role of Computational Design in Peptide Macrocycle Drug Discovery

Expert Opinion on Drug Discovery, 31 Mar 2020
Mulligan VK

Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1

Proc Natl Acad Sci U S A, 23 March 2021
Vikram Khipple Mulligan, Sean Workman, Tianjun Sun, Stephen Rettie, Xinting Li, Liam J Worrall, Timothy W Craven, et al.

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